Noncyclic Notch Activity in the Presomitic Mesoderm Demonstrates Uncoupling of Somite Compartmentalization and Boundary Formation

Total Page:16

File Type:pdf, Size:1020Kb

Noncyclic Notch Activity in the Presomitic Mesoderm Demonstrates Uncoupling of Somite Compartmentalization and Boundary Formation Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION in mice suggested both that FGF signaling acts upstream Noncyclic Notch activity of Notch and Wnt (Wahl et al. 2007) and that Wnt is in the presomitic mesoderm upstream of Notch and FGF (Dunty et al. 2008). Thus, it is still unclear how the activities of the Notch, FGF, and demonstrates uncoupling Wnt pathways are coordinated, and how these pathways of somite compartmentalization contribute to segment border formation and somite pat- terning in mouse embryos. and boundary formation Thus far, the most comprehensively studied genes dis- playing cyclic expression encode components of the Juliane Feller, Andre Schneider,1 Notch pathway. In mice, these are lunatic fringe (Lfng) Karin Schuster-Gossler, and Achim Gossler2 and the bHLH genes Hes1, Hes7, and Hey2 (McGrew et al. 1998; Jouve et al. 2000; Leimeister et al. 2000; Bessho Institute for Molecular Biology, Medizinische Hochschule et al. 2001). Notch1 activity itself oscillates in the pos- Hannover, D-30625 Hanover, Germany terior PSM and appears to be arrested in the anterior PSM through Mesp2-induced repression by Lfng (Morimoto et To test the significance of cyclic Notch activity for so- al. 2005), a glycosyltransferase that modulates the recep- mite formation in mice, we analyzed embryos expressing tiveness of Notch to various ligands (Hicks et al. 2000). activated Notch (NICD) throughout the presomitic me- Lfng expression is regulated by Notch activity (Morales soderm (PSM). Embryos expressing NICD formed up to et al. 2002), and Lfng was proposed to negatively regulate 18 somites. Expression in the PSM of Hes7, Lfng, and Notch1 activity in the PSM and to establish a negative Spry2 was no longer cyclic, whereas Axin2 was ex- feedback loop that drives cyclic Notch activity (Dale et pressed dynamically. NICD expression led to caudaliza- al. 2003; Morimoto et al. 2005). Similarly, Hes7 oscilla- tions are generated by a negative feedback loop of in- tion of somites, and loss of Notch activity to their ros- stable Hes7 protein periodically repressing Hes7 tran- tralization. Thus, segmentation and anterior–posterior scription (Bessho et al. 2001, 2003; Hirata et al. 2004). somite patterning can be uncoupled, differential Notch Mice homozygous for null alleles of Lfng and Hes7, re- signaling is not required to form segment borders, and spectively, display defects in somite compartmentaliza- Notch is unlikely to be the pacemaker of the segmenta- tion, and somites are irregular in form and size (Zhang tion clock. and Gridley 1998; Bessho et al. 2001). Studies in different vertebrate species addressing Supplemental material is available at http://www.genesdev.org. Notch function during somitogenesis have led to various Received March 20, 2008; revised version accepted June 17, views as to the role of Notch in this process. It has been 2008. proposed that the segmentation clock regulates the pe- riodic activation of Notch (Pourquie 1999; Serth et al. 2003), its signaling is required for the synchronization of Somitogenesis subdivides the paraxial mesoderm of ver- the clock in neighboring cells (Jiang et al. 2000; Ozbudak tebrate embryos into a series of homologous subunits, and Lewis 2008), and the Notch pathway is part of the the somites. Somites form sequentially at the anterior oscillator (Holley et al. 2002; Morales et al. 2002; Dale et end of the presomitic mesoderm (PSM). A molecular os- al. 2003; Morimoto et al. 2005; Mara et al. 2007). In cillator referred to as “segmentation clock” directs cy- mouse embryos, extensive genetic studies led to the clic expression of genes in the PSM and is coupled with view that in the anterior PSM, Mesp2-induced down- the progression of somitogenesis. Expression of cyclic regulation of Notch activity leads to somite boundaries genes is coordinated such that one wave of expression where cells with activated Notch1 abut cells with re- passes through the PSM during the formation of one so- pressed Notch1 activity, that the generation of somite mite (Palmeirim et al. 1997; McGrew et al. 1998; Jiang et polarity and borders is coupled, and Notch is part of the al. 2000; Jouve et al. 2000; Aulehla et al. 2003). Microar- core of the segmentation clock (Takahashi et al. 2003; ray studies of the mouse PSM transcriptome showed in Morimoto et al. 2005; Saga 2007). This contrasts with part mutually exclusive activation of the Notch, FGF, recent findings in zebrafish that indicated a role for and Wnt pathways during each cycle, suggesting coordi- Notch signaling merely in the posterior PSM in the syn- nated regulation of these three pathways (Dequeant et al. chronization of cells (Ozbudak and Lewis 2008). To fur- 2006). There is evidence that Wnt activity in the PSM ther study the role of Notch activity in somite formation acts upstream of Notch (Aulehla et al. 2003; Hofmann et and patterning in mice, we analyzed embryos expressing al. 2004). However, cyclic Lfng expression was main- activated Notch (NICD) throughout the PSM. Our re- tained in embryos with constitutive Wnt activity in the sults argue against a role for Notch as a pacemaker of the PSM (Aulehla et al. 2007). Similarly, the epistatic rela- clock, show that the confrontation of domains with and tionship of FGF and Wnt signaling is not clear, as studies without Notch activity is not a prerequisite for border formation, and demonstrate that segmentation and an- terior–posterior somite patterning can be uncoupled. [Keywords: Notch signaling; segmentation; somite patterning; somito- genesis] Results and Discussion 1Present address: Max-Planck-Institut für Herz- und Lungenforschung, D-61231 Bad Nauheim, Germany To activate Notch signaling throughout the PSM, we 2Corresponding author. E-MAIL [email protected]; FAX 49-511-532-4283. generated transgenic mice expressing Cre in the primi- Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.480408. tive streak under the control of regulatory elements of 2166 GENES & DEVELOPMENT 22:2166–2171 © 2008 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/08; www.genesdev.org Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Notch in boundary formation with clearly discernable segment borders (Fig. 1G–K), in- dicating that the presence of activated transgenic Notch (exoNICD) throughout the PSM did not prevent border formation. To address how activation of endogenous Notch1 is affected by exoNICD, we analyzed the presence of en- dogenous NICD using an antibody that specifically rec- ognizes the cleaved form of Notch1 (but not the trans- gene-encoded NICD that lacks the V1744 epitope). In wild-type embryos, activated Notch1 (for clarity, from hereon referred to as endoNICD) was found in the pos- terior PSM in variable patterns, and in one or two bands in the anterior PSM (red lines in Fig. 2A–C), reflecting cyclic Notch activity. In contrast, T-NICD embryos (n = 21) showed one narrow stripe of endoNICD at the anterior end of the PSM (red arrowheads in Fig. 2D,E) that resembled the anterior endoNICD stripe of wild- type embryos, although levels appeared lower. In addi- tion, a subset of T-NICD embryos (n = 13) had an addi- tional weaker, fuzzy endoNICD stripe posterior to the anterior stripe (Fig. 2D, white arrowhead). In the poste- rior PSM region of T-NICD embryos, endoNICD was severely down-regulated (Fig. 2D,E), indicating that acti- vation of Notch1 was disrupted in the T-NICD embryos. The presence of a stripe(s) of endoNICD in the anterior Figure 1. Segmentation in embryos with constitutive Notch activ- ity. (A–F) In situ hybridization of embryos showing expression of the Nicd-Gfp fusion transcript throughout the paraxial mesoderm of T(s)ϻCre; R-NICD embryos (A,B) and up-regulation of Hey1 in the PSM and the somites (C,D) compared with wild-type embryos (E,F). (G,J,L) Scanning electron microscopic pictures illustrating somites in T(s)ϻCre; R-NICD (G,J) and wild-type (L) embryos. (H,I,M,N) He- malaun-stained plastic sections of somites in T(s)ϻCre; R-NICD (H,I) and wild-type (M,N) embryos. (K) Segmented paraxial meso- derm in T(s)ϻCre; R-NICD embryos visualized by Myf5 expression. Developmental stages are indicated on top. Bars: H,I,M,N, 500 µm. the brachyury gene (Stott et al. 1993), and crossed these mice to ROSANICD mice that allow for conditional ex- pression of the constitutively active intracellular do- main of Notch1 (NICD) by Cre-mediated excision of a stop cassette (Murtaugh et al. 2003). Cre activity resulted in reporter gene expression throughout mesodermal tis- sues (Supplemental Fig. 1), and in embryos carrying the ROSANICD allele and the Cre transgene (hereafter re- ferred to as T-NICD embryos), NICD-Gfp fusion tran- scripts were detected throughout the PSM and in Figure 2. Endogenous Notch1 activity in wild-type and mutant somites (Fig. 1A,B). The Notch target Hey1 was strongly embryos. (A–H) Immunohistochemical detection of activated en- up-regulated throughout the paraxial mesoderm of dogenous Notch1 in the PSM. In contrast to wild-type embryos T-NICD embryos (Fig. 1, cf. C,D and E,F) demonstrating (A–C), endogenous Notch1 activity is down-regulated in the poste- activation of the Notch pathway. T-NICD embryos did rior but is found in one or two stripes in the anterior PSM (arrow- heads in D,E) of T(s)ϻCre; R-NICD embryos. (F) Specificity of anti- not complete turning, became severely retarded and dis- body is demonstrated by the lack of staining in T(s)ϻCre; N1loxp/loxP torted after embryonic day 9.5 (E9.5) with impaired elon- embryos. Loss of Dll1 (G)orPofut1 (H) function completely abol- gation of the embryonic axis, and died around E10.5 with ishes Notch1 activity.
Recommended publications
  • Regulation of Cardiac Progenitors by Combination of Mesp1 and ETS
    REGULATION OF CARDIAC PROGENITORS BY COMBINATION OF MESP1 AND ETS TRANSCRIPTION FACTORS A Dissertation by KUO-CHAN WENG Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Fen Wang Co-Chair of Committee, Robert J. Schwartz Committee Members, James F. Martin Jiang Chang Head of Department, Fen Wang May 2014 Major Subject: Medical Science Copyright 2014 Kuo-Chan Weng ABSTRACT Heart disease remains the leading cause of death worldwide. By understanding the regulating networks during cardiac development we can exploit those networks to manipulate adult cells into cardiac progenitors and provide an alternative for repairing diseased hearts. Mesp1 is considered to have critical roles during cardiac development but the molecular mechanisms need to be further studied. The roles of ETS transcription factors have been primarily limited to hematopoietic differentiation and cancer progression. The ETS transcription factors are known to have proliferating roles and were hypothesized to also be involved in cardiac differentiation and may potentially be used for cell reprogramming. The first part of this study characterizes the expression pattern of Mesp1 protein in early mouse embryo from E6.5 to E9.5 and provides a full expression profile in differentiating embryoid bodies in vitro from the undifferentiated stage to Day10. Our work showed Mesp1 expresses in the posterior region of E6.5 embryo then starts migrating through the primitive streak toward anterior mesoderm and endoderm in E7.5. A Mesp1 linage tracing ES cell line was established, and it allowed us to trace the Mesp1 derived cell population.
    [Show full text]
  • Detailed Review Paper on Retinoid Pathway Signalling
    1 1 Detailed Review Paper on Retinoid Pathway Signalling 2 December 2020 3 2 4 Foreword 5 1. Project 4.97 to develop a Detailed Review Paper (DRP) on the Retinoid System 6 was added to the Test Guidelines Programme work plan in 2015. The project was 7 originally proposed by Sweden and the European Commission later joined the project as 8 a co-lead. In 2019, the OECD Secretariat was added to coordinate input from expert 9 consultants. The initial objectives of the project were to: 10 draft a review of the biology of retinoid signalling pathway, 11 describe retinoid-mediated effects on various organ systems, 12 identify relevant retinoid in vitro and ex vivo assays that measure mechanistic 13 effects of chemicals for development, and 14 Identify in vivo endpoints that could be added to existing test guidelines to 15 identify chemical effects on retinoid pathway signalling. 16 2. This DRP is intended to expand the recommendations for the retinoid pathway 17 included in the OECD Detailed Review Paper on the State of the Science on Novel In 18 vitro and In vivo Screening and Testing Methods and Endpoints for Evaluating 19 Endocrine Disruptors (DRP No 178). The retinoid signalling pathway was one of seven 20 endocrine pathways considered to be susceptible to environmental endocrine disruption 21 and for which relevant endpoints could be measured in new or existing OECD Test 22 Guidelines for evaluating endocrine disruption. Due to the complexity of retinoid 23 signalling across multiple organ systems, this effort was foreseen as a multi-step process.
    [Show full text]
  • Table 2. Significant
    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
    [Show full text]
  • Watsonjn2018.Pdf (1.780Mb)
    UNIVERSITY OF CENTRAL OKLAHOMA Edmond, Oklahoma Department of Biology Investigating Differential Gene Expression in vivo of Cardiac Birth Defects in an Avian Model of Maternal Phenylketonuria A THESIS SUBMITTED TO THE GRADUATE FACULTY In partial fulfillment of the requirements For the degree of MASTER OF SCIENCE IN BIOLOGY By Jamie N. Watson Edmond, OK June 5, 2018 J. Watson/Dr. Nikki Seagraves ii J. Watson/Dr. Nikki Seagraves Acknowledgements It is difficult to articulate the amount of gratitude I have for the support and encouragement I have received throughout my master’s thesis. Many people have added value and support to my life during this time. I am thankful for the education, experience, and friendships I have gained at the University of Central Oklahoma. First, I would like to thank Dr. Nikki Seagraves for her mentorship and friendship. I lucked out when I met her. I have enjoyed working on this project and I am very thankful for her support. I would like thank Thomas Crane for his support and patience throughout my master’s degree. I would like to thank Dr. Shannon Conley for her continued mentorship and support. I would like to thank Liz Bullen and Dr. Eric Howard for their training and help on this project. I would like to thank Kristy Meyer for her friendship and help throughout graduate school. I would like to thank my committee members Dr. Robert Brennan and Dr. Lilian Chooback for their advisement on this project. Also, I would like to thank the biology faculty and staff. I would like to thank the Seagraves lab members: Jailene Canales, Kayley Pate, Mckayla Muse, Grace Thetford, Kody Harvey, Jordan Guffey, and Kayle Patatanian for their hard work and support.
    [Show full text]
  • Supplementary Figure S4
    18DCIS 18IDC Supplementary FigureS4 22DCIS 22IDC C D B A E (0.77) (0.78) 16DCIS 14DCIS 28DCIS 16IDC 28IDC (0.43) (0.49) 0 ADAMTS12 (p.E1469K) 14IDC ERBB2, LASP1,CDK12( CCNE1 ( NUTM2B SDHC,FCGR2B,PBX1,TPR( CD1D, B4GALT3, BCL9, FLG,NUP21OL,TPM3,TDRD10,RIT1,LMNA,PRCC,NTRK1 0 ADAMTS16 (p.E67K) (0.67) (0.89) (0.54) 0 ARHGEF38 (p.P179Hfs*29) 0 ATG9B (p.P823S) (0.68) (1.0) ARID5B, CCDC6 CCNE1, TSHZ3,CEP89 CREB3L2,TRIM24 BRAF, EGFR (7p11); 0 ABRACL (p.R35H) 0 CATSPER1 (p.P152H) 0 ADAMTS18 (p.Y799C) 19q12 0 CCDC88C (p.X1371_splice) (0) 0 ADRA1A (p.P327L) (10q22.3) 0 CCNF (p.D637N) −4 −2 −4 −2 0 AKAP4 (p.G454A) 0 CDYL (p.Y353Lfs*5) −4 −2 Log2 Ratio Log2 Ratio −4 −2 Log2 Ratio Log2 Ratio 0 2 4 0 2 4 0 ARID2 (p.R1068H) 0 COL27A1 (p.G646E) 0 2 4 0 2 4 2 EDRF1 (p.E521K) 0 ARPP21 (p.P791L) ) 0 DDX11 (p.E78K) 2 GPR101, p.A174V 0 ARPP21 (p.P791T) 0 DMGDH (p.W606C) 5 ANP32B, p.G237S 16IDC (Ploidy:2.01) 16DCIS (Ploidy:2.02) 14IDC (Ploidy:2.01) 14DCIS (Ploidy:2.9) -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 Log Ratio Log Ratio Log Ratio Log Ratio 12DCIS 0 ASPM (p.S222T) Log Ratio Log Ratio 0 FMN2 (p.G941A) 20 1 2 3 2 0 1 2 3 2 ERBB3 (p.D297Y) 2 0 1 2 3 20 1 2 3 0 ATRX (p.L1276I) 20 1 2 3 2 0 1 2 3 0 GALNT18 (p.F92L) 2 MAPK4, p.H147Y 0 GALNTL6 (p.E236K) 5 C11orf1, p.Y53C (10q21.2); 0 ATRX (p.R1401W) PIK3CA, p.H1047R 28IDC (Ploidy:2.0) 28DCIS (Ploidy:2.0) 22IDC (Ploidy:3.7) 22DCIS (Ploidy:4.1) 18IDC (Ploidy:3.9) 18DCIS (Ploidy:2.3) 17q12 0 HCFC1 (p.S2025C) 2 LCMT1 (p.S34A) 0 ATXN7L2 (p.X453_splice) SPEN, p.P677Lfs*13 CBFB 1 2 3 4 5 6 7 8 9 10 11
    [Show full text]
  • The Regulation of Lunatic Fringe During Somitogenesis
    THE REGULATION OF LUNATIC FRINGE DURING SOMITOGENESIS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Emily T. Shifley ***** The Ohio State University 2009 Dissertation Committee: Approved by Professor Susan Cole, Advisor Professor Christine Beattie _________________________________ Professor Mark Seeger Advisor Graduate Program in Molecular Genetics Professor Michael Weinstein ABSTRACT Somitogenesis is the morphological hallmark of vertebrate segmentation. Somites bud from the presomitic mesoderm (PSM) in a sequential, periodic fashion and give rise to the rib cage, vertebrae, and dermis and muscles of the back. The regulation of somitogenesis is complex. In the posterior region of the PSM, a segmentation clock operates to organize cohorts of cells into presomites, while in the anterior region of the PSM the presomites are patterned into rostral and caudal compartments (R/C patterning). Both of these stages of somitogenesis are controlled, at least in part, by the Notch pathway and Lunatic fringe (Lfng), a glycosyltransferase that modifies the Notch receptor. To dissect the roles played by Lfng during somitogenesis, we created a novel allele that lacks cyclic Lfng expression within the segmentation clock, but that maintains expression during R/C somite patterning (Lfng∆FCE1). Lfng∆FCE1/∆FCE1 mice have severe defects in their anterior vertebrae and rib cages, but relatively normal sacral and tail vertebrae, unlike Lfng knockouts. Segmentation clock function is differentially affected by the ∆FCE1 deletion; during anterior somitogenesis the expression patterns of many clock genes are disrupted, while during posterior somitogenesis, certain clock components have recovered. R/C patterning occurs relatively normally in Lfng∆FCE1/∆FCE1 embryos, likely contributing to the partial phenotype rescue, and confirming that Lfng ii plays separate roles in the two regions of the PSM.
    [Show full text]
  • Modeling the Human Segmentation Clock with Pluripotent Stem Cells 2 3 Mitsuhiro Matsuda1,10, Yoshihiro Yamanaka2,10, Maya Uemura2,3, Mitsujiro Osawa4, 4 Megumu K
    bioRxiv preprint doi: https://doi.org/10.1101/562447; this version posted February 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Modeling the Human Segmentation Clock with Pluripotent Stem Cells 2 3 Mitsuhiro Matsuda1,10, Yoshihiro Yamanaka2,10, Maya Uemura2,3, Mitsujiro Osawa4, 4 Megumu K. Saito4, Ayako Nagahashi4, Megumi Nishio3, Long Guo5, Shiro Ikegawa5, 5 Satoko Sakurai6, Shunsuke Kihara7, Michiko Nakamura6, Tomoko Matsumoto6, Hiroyuki 6 Yoshitomi2,3, Makoto Ikeya6, Takuya Yamamoto6,8, Knut Woltjen6,9, Miki Ebisuya1*, 7 Junya Toguchida2,3, Cantas Alev2* 8 9 1 Laboratory for Reconstitutive Developmental Biology, RIKEN Center for Biosystems 10 Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan. 11 2 Department of Cell Growth and Differentiation, Center for iPS Cell Research and 12 Application (CiRA), Kyoto University, Kyoto 606-8507, Japan. 13 3 Department of Regeneration Science and Engineering, Institute for Frontier Life and 14 Medical Sciences, Kyoto University, Kyoto 606-8507, Japan. 15 4 Department of Clinical Application, Center for iPS Cell Research and Application 16 (CiRA), Kyoto University, Kyoto 606-8507, Japan. 17 5 Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical 18 Sciences (RIKEN IMS), Tokyo 108-8639, Japan. 19 6 Department of Life Science Frontiers, Center for iPS Cell Research and Application 20 (CiRA), Kyoto University, 606-8507, Kyoto 108-8639, Japan. 21 7 Department of Fundamental Cell Technology, Center for iPS Cell Research and 22 Application (CiRA), Kyoto University, Kyoto 606-8507, Japan. 23 8 AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo 100-004, Japan.
    [Show full text]
  • SUPPLEMENTARY DATA Supplementary Table 1. Top Ten
    SUPPLEMENTARY DATA Supplementary Table 1. Top ten most highly expressed protein-coding genes in the EndoC-βH1 cell line. Expression levels provided for non-mitochondrial genes in EndoC-βH1 and the corresponding expression levels in sorted primary human β-cells (1). Ensembl gene ID Gene Name EndoC-βH1 [RPKM] Primary β cells [RPKM] ENSG00000254647.2 INS 8012.452 166347.111 ENSG00000087086.9 FTL 3090.7454 2066.464 ENSG00000100604.8 CHGA 2853.107 1113.162 ENSG00000099194.5 SCD 1411.631 238.714 ENSG00000118271.5 TTR 1312.8928 1488.996 ENSG00000184009.5 ACTG1 1108.0277 839.681 ENSG00000124172.5 ATP5E 863.42334 254.779 ENSG00000156508.13 EEF1A1 831.17316 637.281 ENSG00000112972.10 HMGCS1 719.7504 22.104 ENSG00000167552.9 TUBA1A 689.1415 511.699 ©2016 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db16-0361/-/DC1 SUPPLEMENTARY DATA Supplementary Table 2. List of genes selected for inclusion in the primary screen. Expression levels in EndoC-βH1 and sorted primary human β-cells are shown for all genes targeted for silencing in the primary screen, ordered by locus association (1). For gene selection, the following criteria were applied: we first considered (1) all protein-coding genes within 1 Mb of a type 2 diabetes association signal that (2) had non-zero expression (RPKM > 0) in both EndoC-βH1 and primary human β-cells. Previous studies have shown cis-eQTLs to form a relatively tight, symmetrical distribution around the target-gene transcription start site, and a 1 Mb cut-off is thus likely to capture most effector transcripts subject to cis regulation (2-5).
    [Show full text]
  • Supplementary Data Genbank Or OSE Vs RO NIA Accession Gene Name Symbol FC B-Value H3073C09 11.38 5.62 H3126B09 9.64 6.44 H3073B0
    Supplementary Data GenBank or OSE vs RO NIA accession Gene name Symbol FC B-value H3073C09 11.38 5.62 H3126B09 9.64 6.44 H3073B08 9.62 5.59 AU022767 Exportin 4 Xpo4 9.62 6.64 H3073B09 9.59 6.48 BG063925 Metallothionein 2 Mt2 9.23 18.89 H3064B07 9.21 6.10 H3073D08 8.28 6.10 AU021923 Jagged 1 Jag1 7.89 5.93 H3070D08 7.54 4.58 BG085110 Cysteine-rich protein 1 (intestinal) Crip1 6.23 16.40 BG063004 Lectin, galactose binding, soluble 1 Lgals1 5.95 10.36 BG069712 5.92 2.34 BG076976 Transcribed locus, strongly similar to NP_032521.1 lectin, galactose binding, soluble 1 5.64 8.36 BG062930 DNA segment, Chr 11, Wayne State University 99, expressed D11Wsu99e 5.63 8.76 BG086474 Insulin-like growth factor binding protein 5 Igfbp5 5.50 15.95 H3002d11 5.13 20.77 BG064706 Keratin complex 1, acidic, gene 19 Krt1-19 5.06 9.07 H3007A09 5.05 2.46 H3065F02 4.84 5.43 BG081752 4.81 1.25 H3010E09 4.71 11.90 H3064c11 4.43 1.00 BG069711 Transmembrane 4 superfamily member 9 Tm4sf9 4.29 1.23 BG077072 Actin, beta, cytoplasmic Actb 4.29 3.01 BG079788 Hemoglobin alpha, adult chain 1 Hba-a1 4.26 6.63 BG076798 4.23 0.80 BG074344 Mesothelin Msln 4.22 6.97 C78835 Actin, beta, cytoplasmic Actb 4.16 3.02 BG067531 4.15 1.61 BG073468 Hemoglobin alpha, adult chain 1 Hba-a1 4.10 6.23 H3154H07 4.08 5.38 AW550167 3.95 5.66 H3121B01 3.94 5.94 H3124f12 3.94 5.64 BG073608 Hemoglobin alpha, adult chain 1 Hba-a1 3.84 5.32 BG073617 Hemoglobin alpha, adult chain 1 Hba-a1 3.84 5.75 BG072574 Hemoglobin alpha, adult chain 1 Hba-a1 3.82 5.93 BG072211 Tumor necrosis factor receptor superfamily,
    [Show full text]
  • Heartbreak Hotel: a Convergence in Cardiac Regeneration Michael D
    © 2016. Published by The Company of Biologists Ltd | Development (2016) 143, 1435-1441 doi:10.1242/dev.133652 MEETING REVIEW Heartbreak hotel: a convergence in cardiac regeneration Michael D. Schneider* ABSTRACT along with Tbx6, binds an essential early mesodermal enhancer In February 2016, The Company of Biologists hosted an intimate shared by Mesp1 and Mesp2, and deletion of this element prevents gathering of leading international researchers at the forefront of Mesp1/2 activation, the epithelial-mesenchymal transition, and experimental cardiovascular regeneration, with its emphasis on induction of the cardiovascular progenitors. ‘Transdifferentiation and Tissue Plasticity in Cardiovascular Cardiovascular origins were also discussed by Christian Rejuvenation’. As I review here, participants at the workshop Mosimann (University of Zurich, Switzerland). In vertebrates revealed how understanding cardiac growth and lineage decisions such as zebrafish, lateral plate mesoderm (LPM)-derived cell at their most fundamental level has transformed the strategies in hand types include not only the heart, but also blood vessels, blood, that presently energize the prospects for human heart repair. kidney and pectoral fins. Mosimann described how a 6.5 kb fragment of the zebrafish draculin (drl) upstream region initially KEY WORDS: Cardiomyocyte, Heart, Regenerative medicine, labels all LPM derivatives but becomes restricted just to Stem cells cardiovascular and hematopoietic lineages and, later still in the heart, just to first heart field (FHF) descendants (Mosimann et al., Introduction 2015). Further dissection of the drl locus revealed a pan-LPM The first organ to be fashioned during embryogenesis – the heart – is enhancer plus anterior and posterior LPM enhancers, while drl the organ that contributes most, worldwide, to death, disability and reporter zebrafish showed that regulators of cardiac septation control healthcare system costs (Roth et al., 2015).
    [Show full text]
  • Reprogramming of Lysosomal Gene Expression by Interleukin-4 and Stat6 Brignull Et Al
    Reprogramming of lysosomal gene expression by interleukin-4 and Stat6 Brignull et al. Brignull et al. BMC Genomics 2013, 14:853 http://www.biomedcentral.com/1471-2164/14/853 Brignull et al. BMC Genomics 2013, 14:853 http://www.biomedcentral.com/1471-2164/14/853 RESEARCH ARTICLE Open Access Reprogramming of lysosomal gene expression by interleukin-4 and Stat6 Louise M Brignull1†, Zsolt Czimmerer2†, Hafida Saidi1,3, Bence Daniel2, Izabel Villela4,5, Nathan W Bartlett6, Sebastian L Johnston6, Lisiane B Meira4, Laszlo Nagy2,7 and Axel Nohturfft1* Abstract Background: Lysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illuminate the physiological contexts in which lysosomal genes are coordinately regulated and to identify transcription factors involved in this control. Results: As transcription factors and their target genes are often co-regulated, we performed meta-analyses of array-based expression data to identify regulators whose mRNA profiles are highly correlated with those of a core set of lysosomal genes. Among the ~50 transcription factors that rank highest by this measure, 65% are involved in differentiation or development, and 22% have been implicated in interferon signaling. The most strongly correlated candidate was Stat6, a factor commonly activated by interleukin-4 (IL-4) or IL-13. Publicly available chromatin immunoprecipitation (ChIP) data from alternatively activated mouse macrophages show that lysosomal genes are overrepresented among Stat6-bound targets. Quantification of RNA from wild-type and Stat6-deficient cells indicates that Stat6 promotes the expression of over 100 lysosomal genes, including hydrolases, subunits of the vacuolar H+ ATPase and trafficking factors.
    [Show full text]
  • A Gene Regulation Network Controlled by Celf1 Protein– Rbpj Mrna Interaction in Xenopus Somite Segmentation
    1078 Research Article A gene regulation network controlled by Celf1 protein– rbpj mRNA interaction in Xenopus somite segmentation Marie Cibois1,2,3, Carole Gautier-Courteille1,2, Laurent Kodjabachian3 and Luc Paillard1,2,* 1Universite´ de Rennes 1, Universite´ Europe´enne de Bretagne, Biosit, CS 34317, 35043 Rennes Cedex, France 2CNRS UMR 6290 Institut de Ge´ne´tique et De´veloppement de Rennes, CS 34317, 35043 Rennes Cedex, France 3Institut de Biologie du De´veloppement de Marseille, Aix-Marseille Universite´, CNRS UMR7288, Case 907, 13288 Marseille Cedex 09, France *Author for correspondence ([email protected]) Biology Open 2, 1078–1083 doi: 10.1242/bio.20135629 Received 30th May 2013 Accepted 18th July 2013 Summary Somite segmentation is impaired in Xenopus celf1 morphant FGF pathway antagonized RA signalling through expression of embryos. The Celf1 RNA-binding protein targets bound cyp26a, our results suggest that Rbpj mediates this antagonism. mRNAs for rapid degradation, and antisense approaches Furthermore, they show that the post-transcriptional demonstrated that segmentation defects in celf1 morphants repression exerted by Celf1 on rbpj mRNA is required to were due to a derepression of rbpj mRNA. Rbpj protein is a key keep cyp26a expression under the control of FGF signalling. player of Notch signalling. Because segmentation involves We conclude that rbpj repression by Celf1 is important to complex cross-talk between several signalling pathways, we couple the FGF and RA pathways in Xenopus segmentation. analysed how rbpj derepression impacted these pathways. We found that rbpj derepression stimulated the Notch pathway. ß 2013. Published by The Company of Biologists Ltd. This is an Notch positively controlled the expression of cyp26a, which Open Access article distributed under the terms of the Creative encodes a retinoic acid (RA)-degrading enzyme.
    [Show full text]